Unsorted PBMCs from a CMV seropositive donor

Peripheral blood mononuclear cells (PBMCs) from a CMV seropositive donor were obtained through a collaboration. Cells were labeled with a panel of 12 dCODE™ Dextramer® reagents (Immudex) and 17 TotalSeq™-C antibodies (BioLegend). See details in the Application Note “Redefining Cellular Phenotyping: Comprehensive Characterization and Resolution of the Antigen-Specific T Cell Response”.

Gene Expression, Cell Surface Protein/Immune Receptor Mapping, and TCR Amplified libraries were generated from 17,400 cells (81% viable, expected cell recovery 8,500) as described in the Single Cell V(D)J Reagent Kits User Guide (CG000186 RevA) and sequenced on Illumina NovaSeq 6000 (Gene expression library) and HiSeq4000 (TCR Amplified and Cell Surface Protein/Immune Receptor Mapping libraries).

These libraries were analyzed using the new Cell Ranger multi pipeline, which combines Gene Expression, Cell Surface Protein/Immune Receptor Mapping, and TCR Amplified libraries from the same sample. Cell Ranger multi enables consistent cell calling between gene expression and V(D)J libraries.

Sequencing Configuration

• Gene Expression: Paired-end (28X91), single-indexed sequencing. Read 1: 28 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 91 cycles. Note: Read 1 requirement is 26 bp; 28 bp Read 1 is trimmed by Cell Ranger pipeline.

• TCR Amplified: Paired-end (150x150), single-indexed sequencing. Read 1: 150 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 150 cycles.

• Cell Surface Protein/Immune Receptor Mapping: Paired-end (28X91), single-indexed sequencing. Read 1: 28 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 91 cycles. Note: Read 1 requirement is 26 bp; 28 bp Read 1 is trimmed by Cell Ranger pipeline.

To maintain donor anonymity, sequence data for this sample is not currently available.

This dataset is licensed under the Creative Commons Attribution license.